Variant report

Variant	rs1551210
Chromosome Location	chr12:42865874-42865875
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1051453	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880283	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10880294	0.89[EUR][1000 genomes]
rs11181422	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11181454	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11181463	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11181465	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11181466	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11181467	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11181483	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11181499	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11181501	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11181502	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11181507	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12228205	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12423048	0.83[EUR][1000 genomes]
rs12815283	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12820154	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1669886	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669892	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1669893	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669904	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1669907	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1669910	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1669936	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17551006	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796380	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1796381	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796382	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796384	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1796386	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1796388	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1796394	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1839935	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2178753	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2406674	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2406875	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2600908	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2708058	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708059	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3747557	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3747558	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3747560	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3810793	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4768399	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4768402	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768411	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768413	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55702525	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56051354	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56290913	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61926593	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6582395	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6582398	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7133836	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71453350	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7296357	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7305397	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7307790	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7959338	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7965743	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7969910	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7970003	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1551210	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL
rs1551210	PPHLN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42831800-42876400	Weak transcription	Psoas Muscle	Psoas
2	chr12:42836000-42875800	Weak transcription	Stomach Mucosa	stomach
3	chr12:42837000-42868800	Weak transcription	Esophagus	oesophagus
4	chr12:42850000-42866400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:42853400-42869200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:42854000-42868600	Weak transcription	Right Ventricle	heart
7	chr12:42854200-42867400	Weak transcription	NHLF	lung
8	chr12:42860200-42866800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:42860200-42868800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:42860200-42870400	Weak transcription	Pancreas	Pancrea
11	chr12:42860200-42876200	Weak transcription	Gastric	stomach
12	chr12:42861400-42876000	Weak transcription	Lung	lung
13	chr12:42861600-42866200	Weak transcription	Ovary	ovary
14	chr12:42862400-42866000	Strong transcription	HSMMtube	muscle
15	chr12:42862400-42867200	Genic enhancers	HUVEC	blood vessel
16	chr12:42862400-42867400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:42862800-42876000	Weak transcription	Aorta	Aorta
18	chr12:42863200-42868400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:42863200-42868800	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:42863400-42866000	Weak transcription	Placenta	Placenta
21	chr12:42863400-42866200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:42863400-42866200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:42863400-42866200	Genic enhancers	Primary B cells from peripheral blood	blood
24	chr12:42863400-42866200	Weak transcription	Right Atrium	heart
25	chr12:42863400-42866200	Strong transcription	NH-A	brain
26	chr12:42863400-42866600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr12:42863400-42866600	Weak transcription	NHEK	skin
28	chr12:42863400-42866800	Strong transcription	Fetal Muscle Leg	muscle
29	chr12:42863400-42866800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr12:42863400-42867800	Enhancers	Fetal Kidney	kidney
31	chr12:42863400-42868800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:42863400-42869200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:42863400-42869600	Enhancers	Fetal Heart	heart
34	chr12:42863400-42874200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr12:42863400-42875600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:42863400-42876000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr12:42863600-42866200	Weak transcription	Fetal Intestine Large	intestine
38	chr12:42863600-42867200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:42863800-42866800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:42863800-42867600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:42864000-42866200	Enhancers	GM12878-XiMat	blood
42	chr12:42864000-42866400	Genic enhancers	HUES48 Cell Line	embryonic stem cell
43	chr12:42864000-42866400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
44	chr12:42864000-42866600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:42864000-42868800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:42864000-42869000	Weak transcription	Small Intestine	intestine
47	chr12:42864200-42866200	Weak transcription	Left Ventricle	heart
48	chr12:42864200-42868200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr12:42864200-42868800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr12:42864400-42866600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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